| name | biobakery-databases |
| description | Install and pin bioBakery reference databases for MetaPhlAn and HUMAnN (ChocoPhlAn markers, UniRef gene families, MetaCyc pathways, utility mapping). Use this skill when: (1) Downloading MetaPhlAn/HUMAnN databases, (2) Choosing UniRef90 vs UniRef50, (3) Aligning MetaPhlAn and HUMAnN DB versions, (4) Troubleshooting missing index paths. Upstream: https://github.com/biobakery/MetaPhlAn and https://github.com/biobakery/humann. For Kraken indexes use kraken2. For eggNOG/CARD/GTDB use those skills. For routing use public-databases.
|
| license | MIT |
| category | utilities |
| tags | ["database","bioBakery","ChocoPhlAn","UniRef","MetaPhlAn","HUMAnN"] |
| upstream | https://github.com/biobakery/biobakery |
bioBakery databases (MetaPhlAn / HUMAnN)
Upstream: MetaPhlAn ·
HUMAnN ·
bioBakery: https://huttenhower.sph.harvard.edu/biobakery/
Analytical thinking
MetaPhlAn and HUMAnN results are database-version-dominated. Changing
ChocoPhlAn or UniRef releases can move species/pathway tables more than tweaking
CLI flags.
Keep MetaPhlAn marker DB and HUMAnN nucleotide/protein DBs compatible for
the same study when you report both taxonomy and pathways. Record:
software version + DB names + install paths + download date.
UniRef90 vs UniRef50 is a sensitivity/specificity and disk trade-off — state it
explicitly; do not silently switch mid-cohort.
Prerequisites
| DB | Used by | Notes |
|---|
| MetaPhlAn / ChocoPhlAn markers | metaphlan | Species-level marker genes |
| HUMAnN ChocoPhlAn | humann | Nucleotide mapping |
| UniRef90 or UniRef50 | humann | Translated search / gene families |
| Utility mapping + MetaCyc | humann | Pathway aggregation |
Disk: tens to hundreds of GB depending on UniRef choice.
How to install (HUMAnN helpers)
mkdir -p db/humann
humann_databases --download chocophlan full db/humann
humann_databases --download uniref uniref90_diamond db/humann
humann_databases --download utility_mapping full db/humann
humann_config --update database_folders nucleotide db/humann/chocophlan
humann_config --update database_folders protein db/humann/uniref
humann_config --update database_folders utility_mapping db/humann/utility_mapping
Exact subcommand names can vary by HUMAnN version — verify with
humann_databases --help for your install.
How to install (MetaPhlAn)
mkdir -p db/metaphlan
metaphlan --install --bowtie2db db/metaphlan
Confirm the DB build string printed in MetaPhlAn logs and archive it.
Decision tree
Profiling DB need?
├─ Marker taxonomy only → MetaPhlAn DB (this skill) → metaphlan
├─ Pathways / gene families → HUMAnN DBs (this skill) → humann
├─ Custom / fast k-mer taxonomy → kraken2 indexes (not bioBakery)
└─ Genome taxonomy for MAGs → gtdb / gtdbtk
Verify
metaphlan --version
humann --version
humann_config --print
ls db/metaphlan db/humann | head
Related skills
public-databases · metaphlan · humann · kraken2 · setup
